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On 9/03/2012 11:58 PM, a a wrote:
<blockquote cite="mid:COL118-W55ECB6D09526F932DD0EF4A3540@phx.gbl"
type="cite">
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Hi Mark,
<div><br>
</div>
<div>I did find the directory "<font size="3" face="'Times New
Roman'">gromacs-4.5.5" </font></div>
<div><br>
</div>
<div>However, when I go into this folder, I have problem to do
the "make" command. I found there is no "Make" file inside
the folder. I can only see the following files inside this
folder. Should I do "make clean" then?</div>
<div><br>
</div>
<div>
<div>acinclude.m4 config Doxyfile.in log
share</div>
<div>aclocal.m4 config.log include
Makefile.am src</div>
<div>admin configure INSTALL.automake
Makefile.in tests</div>
<div>AUTHORS configure.ac INSTALL.cmake man</div>
<div>cmake COPYING INSTALL-GPU & nbsp;
README</div>
<div>CMakeLists.txt COPYING-GPU libtool scripts</div>
<div><br>
</div>
<div>Should I do Makefile.am or Makefile.in intead?</div>
</div>
</div>
</blockquote>
<br>
"make clean" is also unnecessary, and won't work until you have done
a configure stage. I suggest you take installation instructions from
the GROMACS webpage, and pick up their tutorial once you have done a
proper installation.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:COL118-W55ECB6D09526F932DD0EF4A3540@phx.gbl"
type="cite">
<div dir="ltr">
<div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Catherine</div>
<div><br>
</div>
<br>
<div>
<hr id="ecxstopSpelling">Date: Fri, 9 Mar 2012 23:22:51
+1100<br>
From: <a class="moz-txt-link-abbreviated" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a><br>
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: Re: [gmx-users] Error Message when installing
GROMACS.<br>
<br>
On 9/03/2012 10:58 PM, a a wrote:
<blockquote
cite="mid:COL118-W36B69648D6ACA19637302DA3540@phx.gbl">
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<div>
<div dir="ltr">Dear Sir/Madam,
<div><br>
</div>
<div>I am trying to install the GROMACS to my new
workstation. As my old one is not belong to me, I
cannot install VMD to it. Please kindly help to
instruct if I did anything wrong here. Many
thanks.</div>
<div>
<div><br>
</div>
<div>Follow the steps in <a moz-do-not-send="true"
href="http://www.cems.uvm.edu/%7Esmanchu/gromacs_installation.html"
style="font-size:10pt" target="_blank">http://www.cems.uvm.edu/~smanchu/gromacs_installation.html</a><span
style="font-size:10pt">, </span><span
style="font-size:10pt">I have done the
installation fftw-3.0.1 at my
"/Catherine/Gromacs/fftw-3.0.1" directory.</span></div>
<div><br>
</div>
<div>Follow the steps in <a moz-do-not-send="true"
href="http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/"
style="font-size:10pt" target="_blank">http://fertoledo.wordpress.com/2012/01/17/how-to-calculate-cosine-content-in-amber/</a>,
i.e. [<span style="font-size:10pt">wget <a
moz-do-not-send="true"
class="ecxmoz-txt-link-freetext"
href="ftp://ftp.gromacs" target="_blank">ftp://ftp.gromacs</a>
.org/pub/gromacs/gromacs-4.5.4.tar.gz], I have
downloaded the gromacs to my
Catherine/Gromacs/ folder.</span></div>
<div><br>
</div>
<div><span style="font-size:10pt">Follow the steps
in </span><a moz-do-not-send="true"
href="http://www.gromacs.org/Downloads/Installation_Instructions"
style="font-size:10pt" target="_blank">http://www.gromacs.org/Downloads/Installation_Instructions</a><span
style="font-size:10pt">, I have start
installing the GROMACS.</span><span
style="font-size:10pt"> </span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-family:'Times
New\00000d\00000a Roman';font-size:12pt">>
tar -xzvf gromacs-4.5.4.tar.gz</span> </div>
<div><span style="font-family:'Times
New\00000d\00000a Roman';font-size:12pt">>
cd </span><span style="font-family:'Times New
Roman';font-size:16px">gromacs-4-5-4</span></div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
The instruction for this command is wrong, because this is
not the directory created by the previous command. Please
inform the author of the tutorial.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:COL118-W36B69648D6ACA19637302DA3540@phx.gbl">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div><span style="font-family:'Times
New\00000d\00000a Roman';font-size:16px">>
make clean</span></div>
<div><font size="3" face="'Times New Roman'">> </font><span
style="font-family:inherit;line-height:1.5;font-size:10pt;border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;font-style:inherit;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline">./configure
--prefix=/usr/local/gromacs
--program-suffix=""</span></div>
<div><span style="background-color:rgb(255,
255,\00000d\00000a
255);font-family:inherit;line-height:1.5;font-size:10pt;border-top-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;font-style:inherit;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline">>
make</span></div>
<div><span style="line-height:19px">> make
install</span></div>
<div><font color="#707070"><span
style="line-height:19px"><b><br>
</b></span></font></div>
<div><font face="'Times New Roman'"><span
style="line-height:19px">However, when I do
make clean, following error message appear.</span></font></div>
<div>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#ff0000" face="'Times New Roman'">make: *** No rule to make target `clean'. Stop.</font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font face="'Times New Roman'">When I continously doing the make after ./configure step, I found the following error messa
ge:</fo
nt></span></pre>
<font face="'Times New Roman'">
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#ff0000" face="'Times New Roman'">make: *** No targets specified and no makefile found. Stop.</font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><font face="'Times New Roman'"><span style="line-height:19px">Could you please kindly instruct if I have done any things stupidly wrong? Following is the log file for the configure.log, please kindly help.</span></font></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><font face="'Times New Roman'"><span style="line-height:19px">Catherine</span></font></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><font face="'Times New Roman'"><span style="line-height:19px">
</span></font></pre>
<div><font face="'Times New Roman'"><span
style="line-height:19px"><br>
</span></font></div>
<div><font face="'Times New Roman'">
<div><br>
</div>
</font></div>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:bas\00000d\00000a eline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#ff0000" face="'Times New Roman'">
</font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;background-clip:initial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#707070" face="Monaco, 'Courier New', Courier, monospace"><b>
</b></font></span></pre>
<pre style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-bottom:1.154em;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:1.538em;padding-right:1.538em;padding-bottom:1.538em;padding-left:1.538em;vertical-align:baseline;background-image:initial;background-attachment:initial;background-origin:initial;background-clip:in\00000d\00000a itial;background-color:rgb(255, 255, 255)"><span style="border-top-width:0px;border-right-width:0px;border-bottom-width:0px;border-left-width:0px;border-style:initial;border-color:initial;margin-right:0px;margin-bottom:0px;margin-left:0px;outline-width:0px;outline-style:initial;outline-color:initial;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;vertical-align:baseline;line-height:19px"><font color="#707070" face="Monaco, 'Courier New', Courier, monospace"><b>
</b></font></span></pre>
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